One independent investor, who wanted to go only by his last name, Patel, said he still has $1.3 million in his MF Global accounts frozen that he will not be able to access despite the judge order earlier this week. Only about $240,000 was moved to over to his new broker, RJ O'Brien, which he is able to access some of.

Another client, Jason Skole is an equity trader and had accounts at MF Global through a personal investment. He had $185,000 in his MF Global account, but now only has $7,500 through a new broker that his open positions were transferred to.

This type of situation is especially hurtful to conservative investors who may have deposited excess cash in their accounts as a safety measure, and now have a majority of that cash stuck at MF Global.